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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 4-42452038-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=42452038&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 42452038,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006095.2",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2839A>C",
"hgvs_p": "p.Asn947His",
"transcript": "NM_006095.2",
"protein_id": "NP_006086.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1164,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000381668.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006095.2"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2839A>C",
"hgvs_p": "p.Asn947His",
"transcript": "ENST00000381668.9",
"protein_id": "ENSP00000371084.5",
"transcript_support_level": 1,
"aa_start": 947,
"aa_end": null,
"aa_length": 1164,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006095.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381668.9"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2794A>C",
"hgvs_p": "p.Asn932His",
"transcript": "ENST00000264449.14",
"protein_id": "ENSP00000264449.10",
"transcript_support_level": 1,
"aa_start": 932,
"aa_end": null,
"aa_length": 1149,
"cds_start": 2794,
"cds_end": null,
"cds_length": 3450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264449.14"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "n.*491A>C",
"hgvs_p": null,
"transcript": "ENST00000514372.5",
"protein_id": "ENSP00000426495.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000514372.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "n.*491A>C",
"hgvs_p": null,
"transcript": "ENST00000514372.5",
"protein_id": "ENSP00000426495.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000514372.5"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2839A>C",
"hgvs_p": "p.Asn947His",
"transcript": "NM_001400024.1",
"protein_id": "NP_001386953.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1164,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001400024.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2839A>C",
"hgvs_p": "p.Asn947His",
"transcript": "ENST00000905753.1",
"protein_id": "ENSP00000575812.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1164,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905753.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2815A>C",
"hgvs_p": "p.Asn939His",
"transcript": "NM_001400025.1",
"protein_id": "NP_001386954.1",
"transcript_support_level": null,
"aa_start": 939,
"aa_end": null,
"aa_length": 1156,
"cds_start": 2815,
"cds_end": null,
"cds_length": 3471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001400025.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2815A>C",
"hgvs_p": "p.Asn939His",
"transcript": "ENST00000905752.1",
"protein_id": "ENSP00000575811.1",
"transcript_support_level": null,
"aa_start": 939,
"aa_end": null,
"aa_length": 1156,
"cds_start": 2815,
"cds_end": null,
"cds_length": 3471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905752.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2794A>C",
"hgvs_p": "p.Asn932His",
"transcript": "NM_001105529.1",
"protein_id": "NP_001098999.1",
"transcript_support_level": null,
"aa_start": 932,
"aa_end": null,
"aa_length": 1149,
"cds_start": 2794,
"cds_end": null,
"cds_length": 3450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001105529.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2794A>C",
"hgvs_p": "p.Asn932His",
"transcript": "NM_001400026.1",
"protein_id": "NP_001386955.1",
"transcript_support_level": null,
"aa_start": 932,
"aa_end": null,
"aa_length": 1149,
"cds_start": 2794,
"cds_end": null,
"cds_length": 3450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001400026.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2794A>C",
"hgvs_p": "p.Asn932His",
"transcript": "ENST00000700470.1",
"protein_id": "ENSP00000515003.1",
"transcript_support_level": null,
"aa_start": 932,
"aa_end": null,
"aa_length": 1149,
"cds_start": 2794,
"cds_end": null,
"cds_length": 3450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000700470.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2683A>C",
"hgvs_p": "p.Asn895His",
"transcript": "ENST00000905751.1",
"protein_id": "ENSP00000575810.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 1112,
"cds_start": 2683,
"cds_end": null,
"cds_length": 3339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905751.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2302A>C",
"hgvs_p": "p.Asn768His",
"transcript": "NM_001400027.1",
"protein_id": "NP_001386956.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 985,
"cds_start": 2302,
"cds_end": null,
"cds_length": 2958,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001400027.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2860A>C",
"hgvs_p": "p.Asn954His",
"transcript": "XM_011513615.2",
"protein_id": "XP_011511917.1",
"transcript_support_level": null,
"aa_start": 954,
"aa_end": null,
"aa_length": 1171,
"cds_start": 2860,
"cds_end": null,
"cds_length": 3516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513615.2"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2860A>C",
"hgvs_p": "p.Asn954His",
"transcript": "XM_011513616.3",
"protein_id": "XP_011511918.1",
"transcript_support_level": null,
"aa_start": 954,
"aa_end": null,
"aa_length": 1171,
"cds_start": 2860,
"cds_end": null,
"cds_length": 3516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513616.3"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2815A>C",
"hgvs_p": "p.Asn939His",
"transcript": "XM_047449508.1",
"protein_id": "XP_047305464.1",
"transcript_support_level": null,
"aa_start": 939,
"aa_end": null,
"aa_length": 1156,
"cds_start": 2815,
"cds_end": null,
"cds_length": 3471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449508.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "c.2368A>C",
"hgvs_p": "p.Asn790His",
"transcript": "XM_047449509.1",
"protein_id": "XP_047305465.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 1007,
"cds_start": 2368,
"cds_end": null,
"cds_length": 3024,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449509.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "n.*120A>C",
"hgvs_p": null,
"transcript": "ENST00000506602.5",
"protein_id": "ENSP00000421164.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000506602.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"hgvs_c": "n.*120A>C",
"hgvs_p": null,
"transcript": "ENST00000506602.5",
"protein_id": "ENSP00000421164.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000506602.5"
}
],
"gene_symbol": "ATP8A1",
"gene_hgnc_id": 13531,
"dbsnp": "rs760015294",
"frequency_reference_population": 0.000028068234,
"hom_count_reference_population": 0,
"allele_count_reference_population": 41,
"gnomad_exomes_af": 0.0000280682,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7839821577072144,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.331,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.284,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.608,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_006095.2",
"gene_symbol": "ATP8A1",
"hgnc_id": 13531,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2839A>C",
"hgvs_p": "p.Asn947His"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}